Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 18 of 27
Found at i:2923280 original size:30 final size:30
Alignment explanation
Indices: 2923240--2923311 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2923230 TTGTTAAGTT
*
2923240 AATTTAAATAATTTAATTTAT-TAATAATAA
1 AATTTTAATAATTTAATTTATATAA-AATAA
* *
2923270 AATTTTAATAATATAATTTATATAAATTAA
1 AATTTTAATAATTTAATTTATATAAAATAA
2923300 AATTTT-ATAATT
1 AATTTTAATAATT
2923312 ACATAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 5 0.14
30 29 0.78
31 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTTTAATAATTTAATTTATATAAAATAA
Found at i:2923312 original size:14 final size:13
Alignment explanation
Indices: 2923263--2923310 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
2923253 TAATTTATTA
2923263 ATAATAAAATTTT
1 ATAATAAAATTTT
*
2923276 AATAATATAATTTAT
1 -ATAATAAAATTT-T
2923291 ATAAATTAAAATTTT
1 AT-AA-TAAAATTTT
2923306 ATAAT
1 ATAAT
2923311 TACATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.03
14 15 0.52
15 6 0.21
16 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATAAAATTTT
Found at i:2923647 original size:34 final size:34
Alignment explanation
Indices: 2923609--2923678 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
2923599 AAAATAACTC
* *
2923609 TTAAT-TATTATTATTATTCAACATAAATATAATT
1 TTAATATA-TATTATTATTCAACATAAAAACAATT
* *
2923643 TTAATATATATTATTATTTAATATAAAAACAATT
1 TTAATATATATTATTATTCAACATAAAAACAATT
2923677 TT
1 TT
2923679 GATAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (34 bp):
TTAATATATATTATTATTCAACATAAAAACAATT
Found at i:2924460 original size:15 final size:14
Alignment explanation
Indices: 2924422--2924479 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
2924412 AATTAAAGTA
*
2924422 TTTTAAATTAAATT
1 TTTTAATTTAAATT
2924436 TTATTAATTTAAATT
1 TT-TTAATTTAAATT
*
2924451 TATTTGATTTATTAATT
1 T-TTTAATTTA--AATT
2924468 TTTTAATTTAAA
1 TTTTAATTTAAA
2924480 AATATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 4 0.11
15 19 0.51
16 9 0.24
17 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTTAATTTAAATT
Found at i:2924499 original size:22 final size:22
Alignment explanation
Indices: 2924474--2924525 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
2924464 AATTTTTTAA
2924474 TTTAAAAATATTTTTATAGTAT
1 TTTAAAAATATTTTTATAGTAT
* * *
2924496 TTT-AAAGT-TTTTTTTATTAT
1 TTTAAAAATATTTTTATAGTAT
2924516 TTTAAAAATA
1 TTTAAAAATA
2924526 AAATATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 13 0.54
21 8 0.33
22 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTAAAAATATTTTTATAGTAT
Found at i:2924674 original size:22 final size:21
Alignment explanation
Indices: 2924630--2924678 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2924620 TACTATCTAA
*
2924630 AATA-AAATCAAAATAAATTT
1 AATAGAAATCAAAATAAATCT
*
2924650 AATAGAAATCAAACTAAAATCT
1 AATAGAAATCAAAAT-AAATCT
2924672 AATAGAA
1 AATAGAA
2924679 CACTACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 9 0.36
22 12 0.48
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.24
Consensus pattern (21 bp):
AATAGAAATCAAAATAAATCT
Found at i:2927160 original size:18 final size:17
Alignment explanation
Indices: 2927139--2927191 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2927129 AATTATTAAT
*
2927139 ATATTAAATTTAATATAA
1 ATATTAAATATAATA-AA
*
2927157 ATA-TAAATATGATAAA
1 ATATTAAATATAATAAA
2927173 ATATATAAATAT-ATAAA
1 ATAT-TAAATATAATAAA
2927190 AT
1 AT
2927192 TACAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 16 0.52
18 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATATTAAATATAATAAA
Found at i:2927172 original size:26 final size:24
Alignment explanation
Indices: 2927126--2927185 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
2927116 TTTTTATAAA
* *
2927126 ATAAATTATTAATATATTAAATTTAAT
1 ATAAA-TATAAATATATTAAA-AT-AT
2927153 ATAAATATAAATATGA-TAAAATAT
1 ATAAATATAAATAT-ATTAAAATAT
2927177 ATAAATATA
1 ATAAATATA
2927186 TAAAATTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 11 0.37
25 1 0.03
26 12 0.40
27 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAAATATAAATATATTAAAATAT
Found at i:2927184 original size:8 final size:8
Alignment explanation
Indices: 2927126--2927189 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
2927116 TTTTTATAAA
2927126 ATAAAT-T
1 ATAAATAT
*
2927133 ATTAATAT
1 ATAAATAT
*
2927141 ATTAAATTT
1 A-TAAATAT
2927150 AATATAA-AT
1 -ATA-AATAT
2927159 ATAAATAT
1 ATAAATAT
2927167 GATAAAATAT
1 -AT-AAATAT
2927177 ATAAATAT
1 ATAAATAT
2927185 ATAAA
1 ATAAA
2927190 ATTACAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 7 0.15
8 18 0.39
9 12 0.26
10 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
ATAAATAT
Found at i:2927400 original size:19 final size:21
Alignment explanation
Indices: 2927371--2927409 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
2927361 ATTTATATTT
2927371 TAAATTATATAAAAT-TTAAA
1 TAAATTATATAAAATATTAAA
2927391 TAAA-TATATAAAATATTAA
1 TAAATTATATAAAATATTAA
2927410 TATTATACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTATATAAAATATTAAA
Found at i:2928031 original size:3 final size:3
Alignment explanation
Indices: 2928023--2928048 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2928013 CAAAGGAAAA
2928023 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2928049 TACCAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2928651 original size:2 final size:2
Alignment explanation
Indices: 2928644--2928679 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2928634 CAACAGCAAA
2928644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2928680 TGCTAATGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2928893 original size:35 final size:35
Alignment explanation
Indices: 2928846--2928920 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
2928836 ATTAATTTTA
*
2928846 TTTTATTAAAATTATTATT-TAAATAATAAAAAT-AT
1 TTTTATTAAAATT-TAATTATAAAT-ATAAAAATAAT
* *
2928881 TTTTATTTAAATTTAATTATAAATATAAATATAAT
1 TTTTATTAAAATTTAATTATAAATATAAAAATAAT
2928916 TTTTA
1 TTTTA
2928921 ATACTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 11 0.31
35 24 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
TTTTATTAAAATTTAATTATAAATATAAAAATAAT
Found at i:2930008 original size:41 final size:43
Alignment explanation
Indices: 2929936--2930018 Score: 120
Period size: 41 Copynumber: 2.0 Consensus size: 43
2929926 AATCGAGTTT
2929936 AAATATAATATTAAATATATTTATTTAAGTTTAATTTA-ATTTG
1 AAATATAATATTAAATATATTTATTTAAGTTT-ATTTATATTTG
2929979 AAATATAA-ATTTAAA-AT-TTTATTTAAGTTTATTTATATTT
1 AAATATAATA-TTAAATATATTTATTTAAGTTTATTTATATTT
2930019 ATAAATGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
40 5 0.13
41 17 0.45
42 3 0.08
43 13 0.34
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (43 bp):
AAATATAATATTAAATATATTTATTTAAGTTTATTTATATTTG
Found at i:2930070 original size:14 final size:13
Alignment explanation
Indices: 2930051--2930099 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2930041 TTTAAGTCTG
2930051 TTTATATTATATTT
1 TTTATATT-TATTT
2930065 TTTATAATTTATTT
1 TTTAT-ATTTATTT
* *
2930079 TTAAAATTTATTT
1 TTTATATTTATTT
*
2930092 TTTTTATT
1 TTTATATT
2930100 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 13 0.45
14 13 0.45
15 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATATTTATTT
Found at i:2930220 original size:25 final size:24
Alignment explanation
Indices: 2930141--2930227 Score: 61
Period size: 25 Copynumber: 3.5 Consensus size: 24
2930131 TTTTAATATT
* *
2930141 TGTATTATAATATTATATATTTTTA
1 TGTAATATAAAATTA-ATATTTTTA
* * *
2930166 TGTTATA-AAAATT-ATATAATATA
1 TGTAATATAAAATTAATAT-TTTTA
**
2930189 TAAAATATAAAATTAATATGTTTTA
1 TGTAATATAAAATTAATAT-TTTTA
2930214 TGTAATAATAAAAT
1 TGTAAT-ATAAAAT
2930228 AGGTCGGGTT
Statistics
Matches: 45, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
22 4 0.09
23 7 0.16
24 11 0.24
25 16 0.36
26 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
TGTAATATAAAATTAATATTTTTA
Found at i:2931183 original size:24 final size:23
Alignment explanation
Indices: 2931149--2931193 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2931139 TAAATTATTG
2931149 TTTATTAATAAAAAATTATTTAAA
1 TTTATTAATAAAAAATT-TTTAAA
* *
2931173 TTTATTTATAAAATATTTTTA
1 TTTATTAATAAAAAATTTTTA
2931194 TTAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTATTAATAAAAAATTTTTAAA
Found at i:2931736 original size:15 final size:16
Alignment explanation
Indices: 2931689--2931736 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
2931679 AGTAAAATTT
*
2931689 TATTTATAA-TTAATAA
1 TATTTA-AACTTATTAA
2931705 TATTTAAACTTTATTAA
1 TATTTAAAC-TTATTAA
2931722 TATTTAAAC-TATTAA
1 TATTTAAACTTATTAA
2931737 ATTAAATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.28
16 6 0.21
17 15 0.52
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAAACTTATTAA
Found at i:2946625 original size:17 final size:17
Alignment explanation
Indices: 2946605--2946642 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2946595 TTTAAAAATT
*
2946605 TTAAATGTT-TAATATCA
1 TTAAAT-TTATAATATAA
2946622 TTAAATTTATAATATAA
1 TTAAATTTATAATATAA
2946639 TTAA
1 TTAA
2946643 TTAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATTTATAATATAA
Found at i:2946651 original size:17 final size:18
Alignment explanation
Indices: 2946613--2946654 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2946603 TTTTAAATGT
* *
2946613 TTAATATCATTAAATTTA
1 TTAATATAATTAAATTAA
2946631 -TAATATAATT-AATTAA
1 TTAATATAATTAAATTAA
2946647 TTAATATA
1 TTAATATA
2946655 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATATAATTAAATTAA
Found at i:2946681 original size:12 final size:12
Alignment explanation
Indices: 2946647--2946684 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2946637 AATTAATTAA
2946647 TTAAT-ATATTT
1 TTAATAATATTT
2946658 TTAAATTAATATTT
1 TT-AA-TAATATTT
2946672 TTAATAATATTT
1 TTAATAATATTT
2946684 T
1 T
2946685 ATTTTATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 11 0.46
13 3 0.12
14 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTAATAATATTT
Found at i:2946723 original size:22 final size:24
Alignment explanation
Indices: 2946695--2946782 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
2946685 ATTTTATCTT
2946695 ATTATTATTAT-ATAA-TAATTTA
1 ATTATTATTATAATAATTAATTTA
* *
2946717 ATTATTA-T-TAAT-TTTAAATT-
1 ATTATTATTATAATAATTAATTTA
2946737 -TTATTATTATAATAATTAATCTTA
1 ATTATTATTATAATAATTAAT-TTA
2946761 ATT-TTATTATAATAATTAATTT
1 ATTATTATTATAATAATTAATTT
2946783 TATATTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
19 6 0.11
20 2 0.04
21 12 0.22
22 11 0.20
23 4 0.07
24 17 0.31
25 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATAATAATTAATTTA
Found at i:2946767 original size:24 final size:25
Alignment explanation
Indices: 2946740--2946793 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 25
2946730 TTAAATTTTA
2946740 TTATTATAATAATTAATCTTA-ATT
1 TTATTATAATAATTAATCTTATATT
*
2946764 TTATTATAATAATTAATTTTATATT
1 TTATTATAATAATTAATCTTATATT
2946789 TTATT
1 TTATT
2946794 GAATGTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTATAATAATTAATCTTATATT
Found at i:2946768 original size:71 final size:71
Alignment explanation
Indices: 2946628--2946781 Score: 163
Period size: 71 Copynumber: 2.2 Consensus size: 71
2946618 ATCATTAAAT
* * * * *
2946628 TTATAATATAATTAATTAATTAATATATTTTTAAATTAATATTTTTAATAATATTTTATTTTATC
1 TTATAATATAATTAATTAATTAATATAATTTTAAATTAATATTATTAATAATAATTAATTTAATC
2946693 TTATTA
66 TTATTA
* * *
2946699 TTATTATATAA-TAATTTAATTATTATTAATTTTAAATT-TTATTATT-ATAATAATTAATCTTA
1 TTATAATATAATTAA-TTAATTAATA-TAATTTTAAATTAATATTATTAATAATAATTAAT-TTA
*
2946761 ATTTTATTA
63 ATCTTATTA
*
2946770 TAATAAT-TAATT
1 TTATAATATAATT
2946782 TTATATTTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
70 16 0.24
71 41 0.60
72 11 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (71 bp):
TTATAATATAATTAATTAATTAATATAATTTTAAATTAATATTATTAATAATAATTAATTTAATC
TTATTA
Found at i:2946775 original size:27 final size:29
Alignment explanation
Indices: 2946715--2946781 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
2946705 TATAATAATT
* *
2946715 TAATTATT-ATTAATTTTAAATTTTATTA
1 TAATAATTAATTAATCTTAAATTTTATTA
*
2946743 TTATAA-TAATTAATCTT-AATTTTATTA
1 TAATAATTAATTAATCTTAAATTTTATTA
2946770 TAATAATTAATT
1 TAATAATTAATT
2946782 TTATATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TAATAATTAATTAATCTTAAATTTTATTA
Found at i:2947061 original size:23 final size:23
Alignment explanation
Indices: 2947021--2947075 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
2947011 TGAGATAAAA
*
2947021 AATTGTTATATAATTAT-AGTAAT
1 AATT-TTATATAAATATAAGTAAT
* *
2947044 AATTTTATATTAAATATAATTGAT
1 AATTTTATA-TAAATATAAGTAAT
2947068 AATTTTAT
1 AATTTTAT
2947076 TAACAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 10 0.37
24 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
AATTTTATATAAATATAAGTAAT
Found at i:2947495 original size:20 final size:20
Alignment explanation
Indices: 2947455--2947495 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2947445 TTTTAGTAAT
* *
2947455 AAAAAATTAAAAGAAAGTAA
1 AAAAAATTAAAACAAAATAA
*
2947475 AAAAAATTCAAACAAAATAA
1 AAAAAATTAAAACAAAATAA
2947495 A
1 A
2947496 TTTAAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAAAATTAAAACAAAATAA
Found at i:2950216 original size:24 final size:24
Alignment explanation
Indices: 2950184--2950229 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2950174 CACACTTTGC
*
2950184 AAATGGGGTTTTATTGAGGACTCT
1 AAATGGGGTTTTATTCAGGACTCT
2950208 AAATGGGGTTTTATTCAGGACT
1 AAATGGGGTTTTATTCAGGACT
2950230 TTATGGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (24 bp):
AAATGGGGTTTTATTCAGGACTCT
Found at i:2952050 original size:125 final size:125
Alignment explanation
Indices: 2951828--2952077 Score: 491
Period size: 125 Copynumber: 2.0 Consensus size: 125
2951818 GGTAGCATAG
2951828 GAACTTGAGAGATAAAACGTAAGCCATCGATAGATGGTGTTTGTGACTTGAGAAACATAGTAGCA
1 GAACTTGAGAGATAAAACGTAAGCCATCGATAGATGGTGTTTGTGACTTGAGAAACATAGTAGCA
2951893 CAATCAGGAAAATATCATAGAGGCATGAATACTAACTCAGGTTTTCAACAAAGAGAGAAC
66 CAATCAGGAAAATATCATAGAGGCATGAATACTAACTCAGGTTTTCAACAAAGAGAGAAC
*
2951953 GAACTTGAGAGATAAAACGTAAGCCATCGATAGATGGTGTTTGTGACTTGTGAAACATAGTAGCA
1 GAACTTGAGAGATAAAACGTAAGCCATCGATAGATGGTGTTTGTGACTTGAGAAACATAGTAGCA
2952018 CAATCAGGAAAATATCATAGAGGCATGAATACTAACTCAGGTTTTCAACAAAGAGAGAAC
66 CAATCAGGAAAATATCATAGAGGCATGAATACTAACTCAGGTTTTCAACAAAGAGAGAAC
2952078 TAACCTTTGC
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.23
Consensus pattern (125 bp):
GAACTTGAGAGATAAAACGTAAGCCATCGATAGATGGTGTTTGTGACTTGAGAAACATAGTAGCA
CAATCAGGAAAATATCATAGAGGCATGAATACTAACTCAGGTTTTCAACAAAGAGAGAAC
Found at i:2954394 original size:24 final size:23
Alignment explanation
Indices: 2954359--2954403 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2954349 CGTTAATTCC
2954359 AAAACATGAAAAAATTCAGAAACA
1 AAAACATGAAAAAATT-AGAAACA
2954383 AAAACACT-AAAAAATTAGAAA
1 AAAACA-TGAAAAAATTAGAAA
2954404 ATTTTGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 14 0.70
25 1 0.05
ACGTcount: A:0.69, C:0.11, G:0.07, T:0.13
Consensus pattern (23 bp):
AAAACATGAAAAAATTAGAAACA
Found at i:2955970 original size:9 final size:9
Alignment explanation
Indices: 2955956--2955994 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
2955946 TAAATTTAAT
2955956 ATTAATTTA
1 ATTAATTTA
2955965 ATTAATTTA
1 ATTAATTTA
*
2955974 TATAATATTTA
1 -ATTA-ATTTA
2955985 ATTAATTTA
1 ATTAATTTA
2955994 A
1 A
2955995 GATTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 15 0.58
10 6 0.23
11 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTAATTTA
Found at i:2955973 original size:20 final size:20
Alignment explanation
Indices: 2955948--2956005 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2955938 AATAAATTTA
2955948 AATTTAATATTAATTTAATT
1 AATTTAATATTAATTTAATT
*
2955968 AATTT-ATATAATATTTAATT
1 AATTTAATATTA-ATTTAATT
*
2955988 AATTTAAGATTAAATTTA
1 AATTTAATATT-AATTTA
2956006 TATCCTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.16
20 18 0.56
21 8 0.25
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AATTTAATATTAATTTAATT
Found at i:2955985 original size:16 final size:16
Alignment explanation
Indices: 2955966--2956008 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2955956 ATTAATTTAA
*
2955966 TTAATTTATATAATAT
1 TTAATTTATATAAGAT
* *
2955982 TTAATTAATTTAAGAT
1 TTAATTTATATAAGAT
*
2955998 TAAATTTATAT
1 TTAATTTATAT
2956009 CCTCTTTTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAATTTATATAAGAT
Found at i:2959885 original size:6 final size:6
Alignment explanation
Indices: 2959858--2959931 Score: 55
Period size: 6 Copynumber: 12.8 Consensus size: 6
2959848 AGAAAAGAAA
* * * *
2959858 GAAGAG GAAAAG GAAG-G G--GAG GAAGAG GAGGAG GAGGAG GAAGAA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
* * * *
2959903 GAAGAA GAAGAA GAAGAT GAAGAA GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
2959932 AGCAGAAGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 2 0.03
6 53 0.91
ACGTcount: A:0.53, C:0.00, G:0.46, T:0.01
Consensus pattern (6 bp):
GAAGAG
Found at i:2959903 original size:3 final size:3
Alignment explanation
Indices: 2959897--2959979 Score: 103
Period size: 3 Copynumber: 27.7 Consensus size: 3
2959887 GGAGGAGGAG
* * *
2959897 GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GAA GCA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * *
2959945 GCA GAA GCA GGA GAA GAA AAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2959980 GGAGGAGGAG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.60, C:0.04, G:0.35, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:2964124 original size:17 final size:17
Alignment explanation
Indices: 2964102--2964135 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2964092 TATTAGTATC
2964102 TTACTAATTTAGAGGTT
1 TTACTAATTTAGAGGTT
2964119 TTACTAATTTAGAGGTT
1 TTACTAATTTAGAGGTT
2964136 CACTTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
TTACTAATTTAGAGGTT
Found at i:2968651 original size:12 final size:12
Alignment explanation
Indices: 2968634--2968659 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2968624 TTTGGCTTCG
2968634 ATATATATAATT
1 ATATATATAATT
2968646 ATATATATAATT
1 ATATATATAATT
2968658 AT
1 AT
2968660 TGGCAGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATATAATT
Found at i:2971656 original size:27 final size:31
Alignment explanation
Indices: 2971603--2971660 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 31
2971593 ATATTTATAG
*
2971603 TAATTATGAATATAATATATGTGATCATAAT
1 TAATTATGAATATAATATATGTAATCATAAT
2971634 TAATTATG-ATA-AA-ATAT-TAATCATAAT
1 TAATTATGAATATAATATATGTAATCATAAT
2971661 ATTAATAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 9 0.35
28 4 0.15
29 2 0.08
30 3 0.12
31 8 0.31
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (31 bp):
TAATTATGAATATAATATATGTAATCATAAT
Found at i:2973854 original size:5 final size:5
Alignment explanation
Indices: 2973844--2973868 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2973834 GGATTTTTCG
2973844 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
2973869 CTCCTACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2975073 original size:19 final size:19
Alignment explanation
Indices: 2975046--2975087 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2975036 TAGTATATAC
*
2975046 TATTTTAAATATATAAAAT-
1 TATTATAAA-ATATAAAATA
*
2975065 TATTATAAAATATTAAATA
1 TATTATAAAATATAAAATA
2975084 TATT
1 TATT
2975088 TATGTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTATAAAATATAAAATA
Found at i:2975090 original size:20 final size:20
Alignment explanation
Indices: 2975046--2975090 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
2975036 TAGTATATAC
2975046 TATTT-TAAATATATAAAAT
1 TATTTATAAATATATAAAAT
*
2975065 TA-TTATAAA-ATATTAAAT
1 TATTTATAAATATATAAAAT
2975083 ATATTTAT
1 -TATTTAT
2975091 GTTGAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 10 0.45
19 8 0.36
20 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTATAAATATATAAAAT
Found at i:2976066 original size:21 final size:21
Alignment explanation
Indices: 2976027--2976075 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2976017 AAAAATTATT
* *
2976027 TAATTAT-TTTATTTTTAAAA
1 TAATTATATATATATTTAAAA
2976047 TAATTATATATATATTTAAAA
1 TAATTATATATATATTTAAAA
*
2976068 TATTTATA
1 TAATTATA
2976076 ATTTTACAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATTATATATATATTTAAAA
Found at i:2976563 original size:2 final size:2
Alignment explanation
Indices: 2976550--2976580 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2976540 TAAATTGCTC
*
2976550 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2976581 GTAAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2980712 original size:28 final size:27
Alignment explanation
Indices: 2980681--2980738 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 27
2980671 TTAATTATAA
2980681 AAATATTTTAATAATATAATGAATGAAT
1 AAATATTTTAATAATATAATGAATG-AT
2980709 AAATATTTTAATAATATAATGAATGAT
1 AAATATTTTAATAATATAATGAATGAT
2980736 AAA
1 AAA
2980739 ATGTGTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (27 bp):
AAATATTTTAATAATATAATGAATGAT
Found at i:2981698 original size:13 final size:13
Alignment explanation
Indices: 2981682--2981718 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2981672 AAAATTTTTT
2981682 AAATATAATTATA
1 AAATATAATTATA
2981695 AAATATAATTATA
1 AAATATAATTATA
*
2981708 ATATATTAATT
1 AAATA-TAATT
2981719 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATAATTATA
Found at i:2988444 original size:17 final size:17
Alignment explanation
Indices: 2988422--2988462 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2988412 ATATATATTT
2988422 ATAATTAAATTTAAATA
1 ATAATTAAATTTAAATA
* *
2988439 ATAATTTAATTTCAATA
1 ATAATTAAATTTAAATA
2988456 A-AATTAA
1 ATAATTAA
2988463 TTCAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAATTTAAATA
Found at i:2989076 original size:17 final size:19
Alignment explanation
Indices: 2989038--2989074 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2989028 ATTATTTTTC
2989038 AATATCACTTTTAATATAT
1 AATATCACTTTTAATATAT
*
2989057 AATATCATTTTTAATATA
1 AATATCACTTTTAATATA
2989075 ATCTTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATCACTTTTAATATAT
Found at i:2995945 original size:13 final size:13
Alignment explanation
Indices: 2995927--2995952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2995917 TAAATTGATT
2995927 TTTATTTTTTTTA
1 TTTATTTTTTTTA
2995940 TTTATTTTTTTTA
1 TTTATTTTTTTTA
2995953 CCCTGGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTTTTTA
Found at i:3002187 original size:15 final size:14
Alignment explanation
Indices: 3002146--3002212 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 14
3002136 GAGAGGGGCC
*
3002146 GAGGAAGAGGAGGA
1 GAGGAAGGGGAGGA
* *
3002160 AAGGAGGGAGGAAGGA
1 GAGGAAGG-GG-AGGA
3002176 GAGGAAGGGGAAGCG-
1 GAGGAAGGGG-AG-GA
3002191 GAGGAAGTGGGAGGA
1 GAGGAAG-GGGAGGA
3002206 GAGGAAG
1 GAGGAAG
3002213 AAGACGCGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 6 0.14
15 23 0.53
16 14 0.33
ACGTcount: A:0.39, C:0.01, G:0.58, T:0.01
Consensus pattern (14 bp):
GAGGAAGGGGAGGA
Found at i:3002688 original size:24 final size:25
Alignment explanation
Indices: 3002638--3002690 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
3002628 TTATATAAAA
* * *
3002638 ATAATTTTAATTATTTAAATATGAT
1 ATAATTATAATTATATAAAAATGAT
*
3002663 ATAATTATAA-TATATAAAAATTAT
1 ATAATTATAATTATATAAAAATGAT
3002687 ATAA
1 ATAA
3002691 AAATAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATAATTATAATTATATAAAAATGAT
Found at i:3002739 original size:55 final size:55
Alignment explanation
Indices: 3002624--3002741 Score: 143
Period size: 55 Copynumber: 2.1 Consensus size: 55
3002614 TTAATTATTT
* * *
3002624 AAAATTATATAAAAATAATTTTAATTATTTAAATATGATATAATTATAATATATA
1 AAAATTATATAAAAATAATTTTAATTACTTAAATATAATAAAATTATAATATATA
*
3002679 AAAATTATATAAAAATAA-TTTAATTCACTTAAATA-AATTAAAATTTTAA-ATAATA
1 AAAATTATATAAAAATAATTTTAATT-ACTTAAATATAA-TAAAATTATAATAT-ATA
*
3002734 TAAATTAT
1 AAAATTAT
3002742 GATTATATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
54 10 0.18
55 45 0.82
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (55 bp):
AAAATTATATAAAAATAATTTTAATTACTTAAATATAATAAAATTATAATATATA
Found at i:3006515 original size:370 final size:369
Alignment explanation
Indices: 3005806--3006538 Score: 1448
Period size: 370 Copynumber: 2.0 Consensus size: 369
3005796 CAGCATGCTA
3005806 CTCAACTTCCTTTTCCTTCTCTCAGTTTGGGAATGGGGCAACATAATTTGACTACATTCCATATA
1 CTCAACTTCCTTTTCCTTCTCTCAGTTTGGGAATGGGGCAACATAATTTGACTACATTCCATATA
*
3005871 TTGTATGAACTATAATTGAAGTTTTCACTGCAATCCCTCTTGCCGCTAGATTGCTATTATGGCCT
66 TTGTACGAACTATAATTGAAGTTTTCACTGCAATCCCTCTTGCCGCTAGATTGCTATTATGGCCT
3005936 TCCGTTTTTTTGCATTTATCCTTGTTTGCATTGACTGCAGAAGCAAATATGTCTTTAAAGAGTGG
131 TCCGTTTTTTTGCATTTATCCTTGTTTGCATTGACTGCAGAAGCAAATATGTCTTTAAAGAGTGG
3006001 ATGACACAAATTTGGCTGTAGTATAGCCAAGTAACTGGTTATCCAAGCTGTTTGTCTTTAAGGTG
196 ATGACACAAATTTGGCTGTAGTATAGCCAAGTAACTGGTTATCCAAGCTGTTTGTCTTTAAGGTG
3006066 TTGATTGTATGATATTTTAAGATGGAAATCTAGAGTCAAGTGTTTGTTTTAGTTAGCTTAGTTCA
261 TTGATTGTATGATATTTTAAGATGGAAATCTAGAGTCAAGTGTTTGTTTTAGTTAGCTTAGTTCA
3006131 AATACCTTTGGTTGTCTTATAACACTAGCAGCTAATAAATCGTG
326 AATACCTTTGGTTGTCTTATAACACTAGCAGCTAATAAATCGTG
3006175 CTCAACTTCCTTTTCCTTCTCTCAGTTTGGGGAATGGGGCAACATAATTTGACTACATTCCATAT
1 CTCAACTTCCTTTTCCTTCTCTCAGTTT-GGGAATGGGGCAACATAATTTGACTACATTCCATAT
3006240 ATTGTACGAACTATAATTGAAGTTTTCACTGCAATCCCTCTTGCCGCTAGATTGCTATTATGGCC
65 ATTGTACGAACTATAATTGAAGTTTTCACTGCAATCCCTCTTGCCGCTAGATTGCTATTATGGCC
3006305 TTCCGTTTTTTTGCATTTATCCTTGTTTGCATTGACTGCAGAAGCAAATATGTCTTTAAAGAGTG
130 TTCCGTTTTTTTGCATTTATCCTTGTTTGCATTGACTGCAGAAGCAAATATGTCTTTAAAGAGTG
3006370 GATGACACAAATTTGGCTGTAGTATAGCCAAGTAACTGGTTATCCAAGCTGTTTGTCTTTAAGGT
195 GATGACACAAATTTGGCTGTAGTATAGCCAAGTAACTGGTTATCCAAGCTGTTTGTCTTTAAGGT
3006435 GTTGATTGTATGATATTTTAAGATGGAAATCTAGAGTCAAGTGTTTGTTTTAGTTAGCTTAGTTC
260 GTTGATTGTATGATATTTTAAGATGGAAATCTAGAGTCAAGTGTTTGTTTTAGTTAGCTTAGTTC
3006500 AAATACCTTTGGTTGTCTTATAACACTAGCAGCTAATAA
325 AAATACCTTTGGTTGTCTTATAACACTAGCAGCTAATAA
3006539 TTGTGCTTCA
Statistics
Matches: 362, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
369 28 0.08
370 334 0.92
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (369 bp):
CTCAACTTCCTTTTCCTTCTCTCAGTTTGGGAATGGGGCAACATAATTTGACTACATTCCATATA
TTGTACGAACTATAATTGAAGTTTTCACTGCAATCCCTCTTGCCGCTAGATTGCTATTATGGCCT
TCCGTTTTTTTGCATTTATCCTTGTTTGCATTGACTGCAGAAGCAAATATGTCTTTAAAGAGTGG
ATGACACAAATTTGGCTGTAGTATAGCCAAGTAACTGGTTATCCAAGCTGTTTGTCTTTAAGGTG
TTGATTGTATGATATTTTAAGATGGAAATCTAGAGTCAAGTGTTTGTTTTAGTTAGCTTAGTTCA
AATACCTTTGGTTGTCTTATAACACTAGCAGCTAATAAATCGTG
Found at i:3007110 original size:52 final size:53
Alignment explanation
Indices: 3007048--3007158 Score: 206
Period size: 52 Copynumber: 2.1 Consensus size: 53
3007038 TGATTGAAAT
*
3007048 TTCTTACATTGCAACATTTTAACCAAGAAAATTTGAGTATCTC-TTTATATAA
1 TTCTTGCATTGCAACATTTTAACCAAGAAAATTTGAGTATCTCTTTTATATAA
3007100 TTCTTGCATTGCAACATTTTAACCAAGAAAATTTGAGTATCTCTTTTATATAA
1 TTCTTGCATTGCAACATTTTAACCAAGAAAATTTGAGTATCTCTTTTATATAA
3007153 TTCTTG
1 TTCTTG
3007159 GATTTAATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 42 0.74
53 15 0.26
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (53 bp):
TTCTTGCATTGCAACATTTTAACCAAGAAAATTTGAGTATCTCTTTTATATAA
Found at i:3008867 original size:2 final size:2
Alignment explanation
Indices: 3008860--3008884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3008850 CAGAGCCACA
3008860 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3008885 ATTTAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3009891 original size:22 final size:22
Alignment explanation
Indices: 3009866--3009915 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3009856 CGTATTTTAT
3009866 AATATATTAAAAAAATAAATAA
1 AATATATTAAAAAAATAAATAA
* * *
3009888 AATA-AATATAAAAATTAATAA
1 AATATATTAAAAAAATAAATAA
3009909 AA-ATATT
1 AATATATT
3009916 CATGAATGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATATATTAAAAAAATAAATAA
Found at i:3010034 original size:23 final size:22
Alignment explanation
Indices: 3010007--3010049 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3009997 TAAAAAAAAT
3010007 TATTTTCTAT-ATTAATATTTATA
1 TATTTT-TATAATTAA-ATTTATA
3010030 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
3010050 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:3011044 original size:25 final size:25
Alignment explanation
Indices: 3011016--3011063 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3011006 ATTATATTCG
*
3011016 TATTTAATATATAATATGTTTAACA
1 TATTTAATATATAATATATTTAACA
*
3011041 TATTTAATATATATTATATTTAA
1 TATTTAATATATAATATATTTAA
3011064 TATGAAGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTAATATATAATATATTTAACA
Found at i:3012056 original size:14 final size:15
Alignment explanation
Indices: 3012025--3012057 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3012015 ATAAATTTTA
3012025 AATTTATTTAATAAT
1 AATTTATTTAATAAT
*
3012040 AATTTTTTTAA-AAT
1 AATTTATTTAATAAT
3012054 AATT
1 AATT
3012058 ATATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTATTTAATAAT
Found at i:3014028 original size:14 final size:14
Alignment explanation
Indices: 3014005--3014052 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
3013995 TATTAATAAA
3014005 AAATAAATTAAATT
1 AAATAAATTAAATT
*
3014019 AAATATATTAAATT
1 AAATAAATTAAATT
*
3014033 ATAATTAAAATCAAATT
1 A-AA-T-AAATTAAATT
3014050 AAA
1 AAA
3014053 CACTATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 14 0.50
15 2 0.07
16 3 0.11
17 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAAATTAAATT
Found at i:3019257 original size:4 final size:4
Alignment explanation
Indices: 3019250--3019300 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
3019240 TATATATATA
* * * *
3019250 ATAG ATAG ATAG ATAG ATAG ACAG ATAG ATAG ATGG ATGG ATTG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
3019298 ATA
1 ATA
3019301 ACAATCTGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:3030610 original size:5 final size:5
Alignment explanation
Indices: 3030595--3030648 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
3030585 AAATTAATTT
* * *
3030595 TAATA TTATA TAATA TAAATA TAATA TAAAAA TAATTA AAATA TAATA
1 TAATA TAATA TAATA T-AATA TAATA T-AATA TAA-TA TAATA TAATA
3030643 TAATA T
1 TAATA T
3030649 TAAAAATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 28 0.70
6 12 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:3030636 original size:22 final size:22
Alignment explanation
Indices: 3030611--3030669 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
3030601 TATATAATAT
3030611 AAATATAATATAAAAATAATTA
1 AAATATAATATAAAAATAATTA
3030633 AAATATAATAT---AAT-ATTA
1 AAATATAATATAAAAATAATTA
*
3030651 AAA-ATTATATAAAAATAAT
1 AAATATAATATAAAAATAAT
3030670 ATCATAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 6 0.19
18 7 0.22
19 3 0.09
20 3 0.09
21 2 0.06
22 11 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATATAATATAAAAATAATTA
Found at i:3030662 original size:17 final size:18
Alignment explanation
Indices: 3030602--3030662 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
3030592 TTTTAATATT
*
3030602 ATATAATATAA-A-TATA
1 ATATAATATAATATTAAA
3030618 ATATAA-A-AATAATTAAA
1 ATATAATATAAT-ATTAAA
3030635 ATATAATATAATATTAAA
1 ATATAATATAATATTAAA
*
3030653 A-ATTATATAA
1 ATATAATATAA
3030663 AAATAATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 2 0.05
15 1 0.03
16 7 0.18
17 17 0.45
18 8 0.21
19 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAATATAATATTAAA
Found at i:3030665 original size:11 final size:11
Alignment explanation
Indices: 3030604--3030671 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
3030594 TTAATATTAT
*
3030604 ATAATATAAAT
1 ATAATATAAAA
3030615 ATAATATAAAA
1 ATAATATAAAA
3030626 ATAAT-TAAAA
1 ATAATATAAAA
3030636 TATAATAT---A
1 -ATAATATAAAA
3030645 AT-AT-TAAAA
1 ATAATATAAAA
*
3030654 ATTATATAAAA
1 ATAATATAAAA
3030665 ATAATAT
1 ATAATAT
3030672 CATAAAGGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 2 0.04
9 4 0.08
10 7 0.15
11 31 0.65
12 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:3030669 original size:28 final size:27
Alignment explanation
Indices: 3030599--3030671 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
3030589 TAATTTTAAT
*
3030599 ATTATAT-AATATAAATATAATATAAAA
1 ATTATATAAAAAT-AATATAATATAAAA
*
3030626 ATAAT-TAAAATATAATATAATATTAAAA
1 ATTATATAAAA-ATAATATAATA-TAAAA
3030654 ATTATATAAAAATAATAT
1 ATTATATAAAAATAATAT
3030672 CATAAAGGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.38
28 18 0.46
29 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTATATAAAAATAATATAATATAAAA
Found at i:3035494 original size:19 final size:19
Alignment explanation
Indices: 3035458--3035496 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3035448 ACTTCGCTGG
*
3035458 AAAATTTATTTTATTATTT
1 AAAATATATTTTATTATTT
3035477 AAAATATATATTTA-TATTT
1 AAAATATAT-TTTATTATTT
3035496 A
1 A
3035497 TAATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAATATATTTTATTATTT
Found at i:3035638 original size:34 final size:32
Alignment explanation
Indices: 3035600--3035671 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 32
3035590 AATAAATTTT
*
3035600 TTTAAAATTATTTATTATTAATT-AAATAAAAATA
1 TTTAAAATTATTAATT-TT-ATTAAAAT-AAAATA
*
3035634 TTTAAAAATTATTAATTTTTTTAAAATAAAATA
1 TTT-AAAATTATTAATTTTATTAAAATAAAATA
3035667 TTTAA
1 TTTAA
3035672 GATGTATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
32 2 0.06
33 11 0.32
34 9 0.26
35 12 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTAAAATTATTAATTTTATTAAAATAAAATA
Found at i:3037744 original size:14 final size:14
Alignment explanation
Indices: 3037719--3037762 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
3037709 AAACTTATTA
*
3037719 AAAAAATTAAATAT
1 AAAAAATAAAATAT
*
3037733 AAAACATAAAATAT
1 AAAAAATAAAATAT
3037747 AAAAAATAAAA-AT
1 AAAAAATAAAATAT
3037760 AAA
1 AAA
3037763 CAAAGACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAAATAAAATAT
Found at i:3038422 original size:3 final size:3
Alignment explanation
Indices: 3038414--3038453 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3038404 CGGTTCTATC
3038414 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3038454 TCCAAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3038464 original size:3 final size:3
Alignment explanation
Indices: 3038458--3038505 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
3038448 CTTCTTTCCA
*
3038458 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3038506 GATATTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3043981 original size:19 final size:18
Alignment explanation
Indices: 3043954--3044009 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
3043944 ATTAAAAGTA
3043954 ATATGAAAAAT-TATAAATT
1 ATAT-AAAAATATATAAA-T
*
3043973 ATGATAAAAATATATGAAT
1 AT-ATAAAAATATATAAAT
3043992 ATATAAAATATATATAAA
1 ATATAAAA-ATATATAAA
3044010 ATAAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 6 0.19
19 19 0.59
20 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
ATATAAAAATATATAAAT
Found at i:3044015 original size:16 final size:19
Alignment explanation
Indices: 3043976--3044018 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 19
3043966 ATAAATTATG
3043976 ATAAAA-ATATATGAATAT
1 ATAAAATATATATGAATAT
3043994 ATAAAATATATAT-AA-A-
1 ATAAAATATATATGAATAT
3044010 ATAAAATAT
1 ATAAAATAT
3044019 TAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.38
17 1 0.04
18 8 0.33
19 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAAATATATATGAATAT
Found at i:3044490 original size:21 final size:21
Alignment explanation
Indices: 3044461--3044500 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3044451 ATTTTCATTT
* *
3044461 TTTATAAAATTTAAAATATTA
1 TTTAAAAAAATTAAAATATTA
*
3044482 TTTAAAAAAATTAAGATAT
1 TTTAAAAAAATTAAAATAT
3044501 GATTCGTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAATTAAAATATTA
Found at i:3045088 original size:126 final size:127
Alignment explanation
Indices: 3044808--3045143 Score: 352
Period size: 126 Copynumber: 2.7 Consensus size: 127
3044798 ATTTTTAATA
* * *
3044808 AAAAATAATATTTAATTAACTTTAAAAAAATTTACATTAA-TAAATTAAA-A-TATTA--AT-TT
1 AAAAATAATATTTAATTAAGTTTAAAAAAA-TTACATTAACAAAATAAAATATTATTATTATGTT
* *
3044867 -TTTAAAA-AAATAAA---T-AATT-AAATTAAAA-GAGTTTATTATTATTTTTTTAATAAAATT
65 ATTTAAAATAAA-AAATTTTAAATTAAAATAAAAATG-GTTTATTATTATATTTTTAATAAAATT
* * *
3044924 AAAAATAATATTTAATTAAGTTTAAAAAAATTATATTAAC-AAATTAAA-ATT-TTATTATGTTT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAAATAAAATATTATTATTATGTTA
*
3044986 TTATAAAAATAAAAAATTTTAAAATATAAAATAAAAATGGTTTTTTATTATAATTTTTAATAAAA
66 TT-T-AAAATAAAAAATTTT-AAAT-TAAAATAAAAATGGTTTATTATTAT-ATTTTTAATAAAA
3045051 -T
126 TT
* *
3045052 -AAAA-AATATTTAATTATGTTTAAAAAATTTACATTAACAAAATAAAATATTAATTATTATGTT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAAATAAAATATT-ATTATTATGTT
3045115 ATTTAAAATAAAAAATTTTAAATTAAAAT
65 ATTTAAAATAAAAAATTTTAAATTAAAAT
3045144 TTTATTAATT
Statistics
Matches: 188, Mismatches: 10, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
115 20 0.11
116 30 0.16
117 2 0.01
118 2 0.01
119 2 0.01
120 1 0.01
121 7 0.04
122 3 0.02
124 1 0.01
126 40 0.21
127 16 0.09
128 38 0.20
129 14 0.07
130 12 0.06
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (127 bp):
AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAAATAAAATATTATTATTATGTTA
TTTAAAATAAAAAATTTTAAATTAAAATAAAAATGGTTTATTATTATATTTTTAATAAAATT
Found at i:3045274 original size:12 final size:12
Alignment explanation
Indices: 3045236--3045268 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3045226 ACTTTCTCTA
*
3045236 TTAAA-TCATCC
1 TTAAATTCAACC
3045247 TTAAATTCAACC
1 TTAAATTCAACC
3045259 TTAAATTCAA
1 TTAAATTCAA
3045269 TTTTAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAATTCAACC
Found at i:3047027 original size:32 final size:34
Alignment explanation
Indices: 3046978--3047049 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
3046968 AATTAAAAAT
*
3046978 ATTAAAATATTAATTTTACAA-TTTTAT-AATTAA
1 ATTAAAATATAAATTTTA-AATTTTTATAAATTAA
3047011 ATTAAAA-ATAAATTTTAAATTTTTATAAATTAA
1 ATTAAAATATAAATTTTAAATTTTTATAAATTAA
3047044 ATTAAA
1 ATTAAA
3047050 TTACATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 2 0.06
32 15 0.42
33 19 0.53
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
ATTAAAATATAAATTTTAAATTTTTATAAATTAA
Found at i:3051602 original size:20 final size:21
Alignment explanation
Indices: 3051570--3051617 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
3051560 TATAAAATTA
3051570 AAAAATAATTAAAAAAGAT-AT
1 AAAAATAATT-AAAAAGATGAT
*
3051591 AAAAATAA-TAAAAATATGAT
1 AAAAATAATTAAAAAGATGAT
3051611 AAAAATA
1 AAAAATA
3051618 TGTAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 7 0.28
20 10 0.40
21 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAAATAATTAAAAAGATGAT
Found at i:3051618 original size:28 final size:26
Alignment explanation
Indices: 3051548--3051643 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 26
3051538 ATAAATTGGT
* *
3051548 ATATAATATAAATATAAAAT-TAAAAA
1 ATATGATAAAAATATAAAATAT-AAAA
* *
3051574 ATAATTAAAAAAGATATAAAAATAATAAAA
1 AT-ATGATAAAA-ATAT-AAAAT-ATAAAA
*
3051604 ATATGATAAAAATATGTAAATATATAAA
1 ATATGATAAAAATAT-AAAATATA-AAA
3051632 ATATGTATAAAA
1 ATATG-ATAAAA
3051644 TAAATTATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
26 2 0.04
27 9 0.16
28 20 0.36
29 18 0.32
30 6 0.11
31 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (26 bp):
ATATGATAAAAATATAAAATATAAAA
Found at i:3051619 original size:11 final size:11
Alignment explanation
Indices: 3051589--3051643 Score: 52
Period size: 9 Copynumber: 5.5 Consensus size: 11
3051579 TAAAAAAGAT
3051589 ATAAAAATA--
1 ATAAAAATATG
3051598 ATAAAAATATG
1 ATAAAAATATG
3051609 ATAAAAATATG
1 ATAAAAATATG
3051620 -T--AAATAT-
1 ATAAAAATATG
3051627 AT-AAAATATG
1 ATAAAAATATG
3051637 TATAAAA
1 -ATAAAA
3051644 TAAATTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 7 0.18
9 15 0.38
10 1 0.03
11 13 0.33
12 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (11 bp):
ATAAAAATATG
Found at i:3051642 original size:19 final size:19
Alignment explanation
Indices: 3051602--3051638 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
3051592 AAAATAATAA
3051602 AAATATGATAAAAATATGT
1 AAATATGATAAAAATATGT
3051621 AAATAT-AT-AAAATATGT
1 AAATATGATAAAAATATGT
3051638 A
1 A
3051639 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AAATATGATAAAAATATGT
Found at i:3051682 original size:27 final size:24
Alignment explanation
Indices: 3051643--3051712 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
3051633 TATGTATAAA
3051643 ATAAATTATTAATATATAATATTTTAT
1 ATAAATTATTAATA-AT-ATATTTT-T
3051670 ATAAATT-TATAATAATATATTTTT
1 ATAAATTAT-TAATAATATATTTTT
* *
3051694 AT-AATAATTAAAAATATAT
1 ATAAATTATTAATAATATAT
3051713 AAAAACACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 13 0.33
24 4 0.10
25 7 0.18
26 3 0.08
27 12 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAAATTATTAATAATATATTTTT
Found at i:3051709 original size:23 final size:25
Alignment explanation
Indices: 3051645--3051712 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
3051635 TGTATAAAAT
3051645 AAATTATTAATATATAATATTTTATATA
1 AAATTA-TAATA-AT-ATATTTTATATA
*
3051673 AATTTATAATAATATATTTT-TATA
1 AAATTATAATAATATATTTTATATA
3051697 ATAATTA-AA-AATATAT
1 A-AATTATAATAATATAT
3051713 AAAAACACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 7 0.19
24 7 0.19
25 11 0.30
26 2 0.05
27 5 0.14
28 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATTATAATAATATATTTTATATA
Found at i:3052047 original size:12 final size:12
Alignment explanation
Indices: 3052026--3052062 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3052016 TTGAGTATAC
3052026 ATTT-TAAATTA
1 ATTTATAAATTA
3052037 ATTTATAAATTA
1 ATTTATAAATTA
*
3052049 ATATATAAATTA
1 ATTTATAAATTA
3052061 AT
1 AT
3052063 CATTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTATAAATTA
Found at i:3052375 original size:19 final size:17
Alignment explanation
Indices: 3052334--3052376 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
3052324 ATAAAATTAA
3052334 AATAAAAATATACAAAT
1 AATAAAAATATACAAAT
*
3052351 ATATAAAATATATATTAAAT
1 A-ATAAAA-ATATA-CAAAT
3052371 AATAAA
1 AATAAA
3052377 TTATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 10 0.45
20 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAAATATACAAAT
Found at i:3054108 original size:3 final size:3
Alignment explanation
Indices: 3054100--3054148 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3054090 GTAATAGAAG
3054100 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3054148 A
1 A
3054149 GAAGAAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3054153 original size:3 final size:3
Alignment explanation
Indices: 3054147--3054181 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3054137 TAATAATAAT
3054147 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3054182 AATGAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3055666 original size:2 final size:2
Alignment explanation
Indices: 3055661--3055687 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3055651 ACATACGTAC
3055661 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3055688 ACTGCAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3058854 original size:28 final size:27
Alignment explanation
Indices: 3058814--3058871 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
3058804 TTTTAATATC
* *
3058814 TAAATTTTTTAATCATAAATAAATAAAA
1 TAAATATTATAATCATAAA-AAATAAAA
** *
3058842 TAAATATTATAATGTTAAAAAATATAA
1 TAAATATTATAATCATAAAAAATAAAA
3058869 TAA
1 TAA
3058872 GTTATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATATTATAATCATAAAAAATAAAA
Found at i:3058965 original size:11 final size:11
Alignment explanation
Indices: 3058941--3058973 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3058931 AATTTGTACC
*
3058941 ATTAAAAAAT-
1 ATTAAAAATTA
3058951 ATTAAAAATTA
1 ATTAAAAATTA
3058962 ATTAAAAATTA
1 ATTAAAAATTA
3058973 A
1 A
3058974 ATAAGTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAAAATTA
Found at i:3060045 original size:26 final size:25
Alignment explanation
Indices: 3060012--3060062 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3060002 ATTAAATTAA
3060012 TTTTATATAAATATAAATAAATATT
1 TTTTATATAAATATAAATAAATATT
* * *
3060037 TTTTCATATATATATATATACATATT
1 TTTT-ATATAAATATAAATAAATATT
3060063 ATAACCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTATATAAATATAAATAAATATT
Found at i:3061080 original size:14 final size:15
Alignment explanation
Indices: 3061063--3061093 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3061053 AATTAAATTA
3061063 AATTTT-ATATTTTT
1 AATTTTAATATTTTT
3061077 AATTTTAATATTTTT
1 AATTTTAATATTTTT
3061092 AA
1 AA
3061094 AATTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTAATATTTTT
Found at i:3064899 original size:14 final size:14
Alignment explanation
Indices: 3064882--3064939 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
3064872 TTATTCAAAA
*
3064882 AATATTTTTATATT
1 AATATTTATATATT
3064896 AATATTTATATAATT
1 AATATTTATAT-ATT
*
3064911 AA-ATTTAAATA-T
1 AATATTTATATATT
*
3064923 AATAATTT-TTTATT
1 AAT-ATTTATATATT
3064937 AAT
1 AAT
3064940 TAACCAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 25 0.69
15 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:3069847 original size:15 final size:15
Alignment explanation
Indices: 3069827--3069865 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3069817 CTAATATTAT
3069827 ATATTTATATGTATA
1 ATATTTATATGTATA
*
3069842 ATATTTATATATATA
1 ATATTTATATGTATA
3069857 A-A-TTATATG
1 ATATTTATATG
3069866 ATTGAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 1 0.05
15 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATATTTATATGTATA
Found at i:3070349 original size:18 final size:19
Alignment explanation
Indices: 3070318--3070353 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3070308 AATATTGTAG
3070318 ATATAGATTATAAAATATA
1 ATATAGATTATAAAATATA
3070337 ATATAGA-TATAAAATAT
1 ATATAGATTATAAAATAT
3070354 TATAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
ATATAGATTATAAAATATA
Found at i:3071937 original size:19 final size:19
Alignment explanation
Indices: 3071883--3071957 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
3071873 ATTCATGATA
*
3071883 AAATTTTTTAATTTTATAATT
1 AAATATTTTAATTTT-T-ATT
* *
3071904 -AA-ATTTAAATATTTATT
1 AAATATTTTAATTTTTATT
3071921 AAATATTTTAATTTTTA--
1 AAATATTTTAATTTTTATT
3071938 AAATTATTTTTAATTTTTAT
1 AAA-TA-TTTTAATTTTTAT
3071958 ATTTTTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.14
18 5 0.11
19 31 0.70
20 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATATTTTAATTTTTATT
Found at i:3071937 original size:27 final size:26
Alignment explanation
Indices: 3071907--3071966 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 26
3071897 TATAATTAAA
3071907 TTTAAA-TATTTATTAAATATTTTA-ATT
1 TTTAAATTATTT-TT-AAT-TTTTATATT
3071934 TTTAAAATTATTTTTAATTTTTATATT
1 TTT-AAATTATTTTTAATTTTTATATT
3071961 TTTAAA
1 TTTAAA
3071967 AAAAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 8 0.27
27 12 0.40
28 5 0.17
29 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTAAATTATTTTTAATTTTTATATT
Found at i:3072417 original size:19 final size:19
Alignment explanation
Indices: 3072395--3072450 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
3072385 AAAATTATAG
3072395 TATTATATTAATATTTAAA
1 TATTATATTAATATTTAAA
*
3072414 TATT-TATTAA-ATATAAA
1 TATTATATTAATATTTAAA
*
3072431 TATTATTAATAAATATTTAA
1 TATTA-T-ATTAATATTTAA
3072451 TAAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 5 0.17
20 4 0.13
21 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTATATTAATATTTAAA
Found at i:3072716 original size:11 final size:11
Alignment explanation
Indices: 3072700--3072732 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3072690 ATAGACTTAG
3072700 AAAAAAA-AAA
1 AAAAAAAGAAA
3072710 AAAAAAAGAAA
1 AAAAAAAGAAA
*
3072721 AAGAAAAGAAA
1 AAAAAAAGAAA
3072732 A
1 A
3072733 GAAGCACCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:3072727 original size:16 final size:16
Alignment explanation
Indices: 3072702--3072735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3072692 AGACTTAGAA
3072702 AAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
* *
3072718 AAAAAGAAAAGAAAAG
1 AAAAAAAAAAAAAAAG
3072734 AA
1 AA
3072736 GCACCGGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:3076833 original size:2 final size:2
Alignment explanation
Indices: 3076826--3076856 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3076816 AAAAGTTCAA
3076826 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3076857 AGAAGACTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3079060 original size:53 final size:53
Alignment explanation
Indices: 3078980--3079085 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
3078970 GATTGTATTT
* *
3078980 CAAATAAACTAGTATGTTATAGCAAGCATGATAGAATCTGAAATTCCAAATTC
1 CAAATAAACTAGAATGTTATAGCAAGCATGATAGAAACTGAAATTCCAAATTC
3079033 CAAATAAACTAGAATGTTATAGCAAGCATGATAGAAACTGAAATTCCAAATTC
1 CAAATAAACTAGAATGTTATAGCAAGCATGATAGAAACTGAAATTCCAAATTC
3079086 TTCATGAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (53 bp):
CAAATAAACTAGAATGTTATAGCAAGCATGATAGAAACTGAAATTCCAAATTC
Found at i:3083938 original size:2 final size:2
Alignment explanation
Indices: 3083926--3083960 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3083916 GCTTCTGAAT
*
3083926 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3083961 CTGAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3087543 original size:15 final size:16
Alignment explanation
Indices: 3087523--3087552 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3087513 TCATCTCCCC
3087523 AGATCTA-CTTGCATG
1 AGATCTAGCTTGCATG
3087538 AGATCTAGCTTGCAT
1 AGATCTAGCTTGCAT
3087553 ATAATAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (16 bp):
AGATCTAGCTTGCATG
Found at i:3090550 original size:15 final size:15
Alignment explanation
Indices: 3090509--3090554 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3090499 ACAATTTAAA
3090509 TTATATAATATATATT
1 TTATA-AATATATATT
*
3090525 TATAAAAATATATATT
1 T-TATAAATATATATT
3090541 TTATAAATATATAT
1 TTATAAATATATAT
3090555 AAATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 12 0.44
16 12 0.44
17 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATAAATATATATT
Found at i:3090577 original size:16 final size:17
Alignment explanation
Indices: 3090496--3090579 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 17
3090486 ATGCATCTTC
3090496 TATACAATTTAAATTATATAA
1 TATA-AATTTAAA--ATA-AA
* *
3090517 TATATATTTATAA-AAA
1 TATAAATTTAAAATAAA
* *
3090533 TATATATTTTATAAATATA
1 TATA-AATTTA-AAATAAA
3090552 TATAAA-TTAAAATAAA
1 TATAAATTTAAAATAAA
3090568 T-TAAATTTAAAA
1 TATAAATTTAAAA
3090580 CTTAAATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
15 4 0.08
16 19 0.37
17 8 0.16
18 4 0.08
19 6 0.12
20 6 0.12
21 4 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAAATTTAAAATAAA
Found at i:3090586 original size:13 final size:13
Alignment explanation
Indices: 3090544--3090597 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
3090534 ATATATTTTA
3090544 TAAATATATATAAAT
1 TAAATAT-TA-AAAT
3090559 TAAA-A-T-AAAT
1 TAAATATTAAAAT
3090569 TAAAT-TTAAAACT
1 TAAATATTAAAA-T
3090582 TAAATATTAAAAT
1 TAAATATTAAAAT
3090595 TAA
1 TAA
3090598 GATCCAACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 4 0.12
13 10 0.29
14 7 0.21
15 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATATTAAAAT
Found at i:3091319 original size:10 final size:10
Alignment explanation
Indices: 3091304--3091330 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3091294 TTATTAGTCA
3091304 TTAAGTCGAT
1 TTAAGTCGAT
3091314 TTAAGTCGAT
1 TTAAGTCGAT
3091324 TTAAGTC
1 TTAAGTC
3091331 TTTGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (10 bp):
TTAAGTCGAT
Found at i:3091535 original size:7 final size:7
Alignment explanation
Indices: 3091511--3091552 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
3091501 TTGTTAAGCT
3091511 AAAAAATG
1 AAAAAA-G
3091519 AAAGAAAG
1 AAA-AAAG
3091527 AAAAAAG
1 AAAAAAG
3091534 -AAAAAG
1 AAAAAAG
*
3091540 AAAAAAT
1 AAAAAAG
3091547 AAAAAA
1 AAAAAA
3091553 AAATTAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
6 6 0.19
7 15 0.48
8 7 0.23
9 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:3091541 original size:13 final size:13
Alignment explanation
Indices: 3091523--3091555 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3091513 AAAATGAAAG
3091523 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
*
3091536 AAAGAAAAAATAA
1 AAAGAAAAAAGAA
3091549 AAA-AAAA
1 AAAGAAAA
3091556 TTAAGGATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:3091597 original size:20 final size:22
Alignment explanation
Indices: 3091572--3091623 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3091562 ATCCGTATTT
3091572 TATTATTTTTATAT-TTAA-AA
1 TATTATTTTTATATATTAATAA
3091592 TATTATATTTTTATATATTAATAA
1 TA-T-TATTTTTATATATTAATAA
3091616 T-TTATTTT
1 TATTATTTT
3091624 ATTTTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 2 0.07
21 7 0.25
22 12 0.43
23 4 0.14
24 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTTTTATATATTAATAA
Found at i:3091603 original size:23 final size:23
Alignment explanation
Indices: 3091570--3091653 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
3091560 GGATCCGTAT
3091570 TTTATTATTTTTATAT-TTAA-AA
1 TTTA-TATTTTTATATATTAATAA
3091592 TATTATATTTTTATATATTAATAA
1 T-TTATATTTTTATATATTAATAA
*
3091616 TTTAT-TTTATTTTATA-T-AT-A
1 TTTATATTT-TTATATATTAATAA
* *
3091636 TTTATATGTATATATATT
1 TTTATATTTTTATATATT
3091654 CATATTATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 11 0.21
21 5 0.10
22 16 0.31
23 17 0.33
24 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (23 bp):
TTTATATTTTTATATATTAATAA
Found at i:3091658 original size:16 final size:16
Alignment explanation
Indices: 3091628--3091658 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3091618 TATTTTATTT
*
3091628 TATATATATTTATATG
1 TATATATATTCATATG
3091644 TATATATATTCATAT
1 TATATATATTCATAT
3091659 TATGTGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATATTCATATG
Found at i:3091672 original size:19 final size:19
Alignment explanation
Indices: 3091656--3091736 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 19
3091646 TATATATTCA
3091656 TATTATGTGTTATTATTAT
1 TATTATGTGTTATTATTAT
* *
3091675 TATTATTTTTTATTATCTATT
1 TATTATGTGTTATTAT-TA-T
* *
3091696 TATTTATATCTATATTTATTAT
1 TA-TTATGTGT-TA-TTATTAT
*
3091718 TATTAT-TATTATTTATTAT
1 TATTATGTGTTA-TTATTAT
3091737 CTATCTATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
19 24 0.46
20 4 0.08
21 7 0.13
22 9 0.17
23 4 0.08
24 4 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTATGTGTTATTATTAT
Found at i:3091673 original size:3 final size:3
Alignment explanation
Indices: 3091665--3091736 Score: 62
Period size: 3 Copynumber: 23.3 Consensus size: 3
3091655 ATATTATGTG
3091665 TTA TTA TTA TTA TTA TT- TT- TTA TTA TCTA TTTA TT- TATA TCTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA T-TA T-TA TTA
3091710 TTTA TTA TTA TTA TTA TTA TTTA TTA T
1 -TTA TTA TTA TTA TTA TTA -TTA TTA T
3091737 CTATCTATCT
Statistics
Matches: 60, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
2 7 0.12
3 40 0.67
4 12 0.20
5 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3091705 original size:14 final size:14
Alignment explanation
Indices: 3091671--3091740 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 14
3091661 TGTGTTATTA
3091671 TTATTAT-TATTTT
1 TTATTATCTATTTT
3091684 TTATTATCTATTTAT
1 TTATTATCTATTT-T
3091699 TTA-TATCTATATTT
1 TTATTATCTAT-TTT
3091713 ATTATTAT-TATTATTAT
1 -TTATTATCTA-T-TT-T
3091730 TTATTATCTAT
1 TTATTATCTAT
3091741 CTATCTATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.14
14 13 0.27
15 11 0.22
16 15 0.31
17 3 0.06
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATCTATTTT
Found at i:3091715 original size:46 final size:46
Alignment explanation
Indices: 3091665--3091754 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
3091655 ATATTATGTG
* * * *
3091665 TTATTATTATTATTATTTTTTATTATCTATTTATTTATATCTATAT
1 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
3091711 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
1 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
3091755 CTAACATGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (46 bp):
TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
Found at i:3092206 original size:2 final size:2
Alignment explanation
Indices: 3092199--3092231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3092189 CATATAGATT
3092199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3092232 GCAAAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3092899 original size:12 final size:13
Alignment explanation
Indices: 3092882--3092910 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3092872 AAATTTTATG
3092882 TTTTTATA-TTTA
1 TTTTTATATTTTA
3092894 TTTTTATATTTTA
1 TTTTTATATTTTA
3092907 TTTT
1 TTTT
3092911 AATTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATATTTTA
Found at i:3093079 original size:38 final size:37
Alignment explanation
Indices: 3092993--3093105 Score: 102
Period size: 39 Copynumber: 2.9 Consensus size: 37
3092983 CATATTAATT
* *
3092993 ATTTATTTATATATAT-TTTTAATATATTTATATATTCAG
1 ATTTGTTTATAT-TATGTTTTAAT-TATTT-TATATTTAG
* * *
3093032 ATTTTTTTATATTATGTTTTAATTATTTTCTATTTAT
1 ATTTGTTTATATTATGTTTTAATTATTTTATATTTAG
** *
3093069 ATTATGTTTATATCGTGTCTTAATTTATTTTATATTT
1 ATT-TGTTTATATTATGTTTTAA-TTATTTTATATTT
3093106 TTTTACATAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
37 9 0.15
38 23 0.37
39 30 0.48
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (37 bp):
ATTTGTTTATATTATGTTTTAATTATTTTATATTTAG
Found at i:3093998 original size:7 final size:7
Alignment explanation
Indices: 3093986--3094025 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
3093976 AAAAACTTCA
3093986 TATTTTT
1 TATTTTT
3093993 TA-TTTT
1 TATTTTT
3093999 TATTTTT
1 TATTTTT
3094006 TATTTTT
1 TATTTTT
*
3094013 TAATTTT
1 TATTTTT
*
3094020 AATTTT
1 TATTTT
3094026 ATTTTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TATTTTT
Done.